Taxonomy Profiling and Visualization with Krona

microbiome-pathogen-detection-from-nanopore-foodborne-data/taxonomy-profiling-and-visualisation-with-krona

Author(s)
Engy Nasr, Bérénice Batut, Paul Zierep
Version
2
Last updated
Jun 6, 2024
License
MIT
Tags
name:Collection
name:microGalaxy
name:PathoGFAIR
name:IWC

Features
Tutorial
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00145
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Collection\ncollection_of_preprocessed_samples"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nkraken_database"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["Kraken2"];
  1 -->|output| 2;
  0 -->|output| 2;
  26f9041f-d8a4-4f64-8a53-404d5c7e2f61["Output\nkraken2_with_pluspf_database_output"];
  2 --> 26f9041f-d8a4-4f64-8a53-404d5c7e2f61;
  style 26f9041f-d8a4-4f64-8a53-404d5c7e2f61 stroke:#2c3143,stroke-width:4px;
  f2ddd05b-66a0-4cea-9da6-ed107eecbe1b["Output\nkraken2_with_pluspf_database_output_report"];
  2 --> f2ddd05b-66a0-4cea-9da6-ed107eecbe1b;
  style f2ddd05b-66a0-4cea-9da6-ed107eecbe1b stroke:#2c3143,stroke-width:4px;
  3["Krakentools: Convert kraken report file"];
  2 -->|report_output| 3;
  c490ab8d-1b1d-4914-aa51-a62a967a4018["Output\nconverted_kraken_report"];
  3 --> c490ab8d-1b1d-4914-aa51-a62a967a4018;
  style c490ab8d-1b1d-4914-aa51-a62a967a4018 stroke:#2c3143,stroke-width:4px;
  4["Krona pie chart"];
  3 -->|output| 4;
  dcc857c6-f579-4c74-84ec-bb6ce3794a56["Output\nkrona_pie_chart"];
  4 --> dcc857c6-f579-4c74-84ec-bb6ce3794a56;
  style dcc857c6-f579-4c74-84ec-bb6ce3794a56 stroke:#2c3143,stroke-width:4px;

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
2 cdd93376a 2024-06-06 12:00:29 adding tags to some of the workflow outputs, updating the training with the latest PathoGFAIR workflows updates
1 c63ce23c7 2024-05-26 12:29:47 updating workflows file names

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/taxonomy_profiling_and_visualisation_with_krona.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows